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Sample GSM80321 Query DataSets for GSM80321
Status Public on Oct 28, 2005
Title ZFL T2+
Sample type RNA
 
Channel 1
Source name Zebrafish liver tissue
Organism Danio rerio
Characteristics Zebrafish liver tumor tissue or normal liver tissue
Growth protocol Zebrafish were reared at room temperature (27 ± 2°C)
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy5
Label protocol For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy5-dUTP (Amersham Inc.). Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
Channel 2
Source name Zebrafish normal liver tissue
Organism Danio rerio
Characteristics Reference RNA was obtained by pooling equal amount of male total RNA extracted from liver tissues of wild-type zebrafish.
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy3
Label protocol For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP (Amersham Inc.). Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
 
Scan protocol The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).
Description Zebrafish liver tumor tissue (induced by carcinogens) vs zebrafish normal liver tissue.
Data processing Data processing The data were global median normalized.Normalized ratio of means defined by CH1/CH2
 
Submission date Oct 27, 2005
Last update date Oct 27, 2005
Contact name Siew Hong Lam
E-mail(s) dbslsh@nus.edu.sg
Phone (65)- 68742860
Fax (65)-67792486
Organization name National University of Singapore
Department Biological Sciences
Street address 14 Science Drive 4
City Singapore
ZIP/Postal code 117543
Country Singapore
 
Platform ID GPL2715
Series (1)
GSE3519 Molecular Conservation of Zebrafish and Human Liver Tumors.

Data table header descriptions
ID_REF Unique ID
VALUE log2 of PRE_VALUE
CH1_Median CH1(F635) median fluorescence intensity
CH1_MEAN CH1 (F635) mean fluorescence intensity
CH1_SD CH1 (F635) fluorescence intensity standard deviation
CH1_BKD_Median CH1 (F635) background median fluorescence intensity
CH1_BKD_MEAN CH1 (F635) background mean fluorescence intensity
CH1_BKD_SD CH1 (F635) background fluorescence intensity standard deviation
%>CH1_BKD_+2SD % of feature pixels greater than two standard deviations over the background
CH2_Median CH2(F532) median fluorescence intensity
CH2_MEAN CH2 (F532) mean fluorescence intensity
CH2_SD CH2 (F532) fluorescence intensity standard deviation
CH2_BKD_Median CH2 (F532) background median fluorescence intensity
CH2_BKD_MEAN CH2 (F532) background mean fluorescence intensity
CH2_BKD_SD CH2 (F532) background fluorescence intensity standard deviation
%>CH2_BKD_+2SD % of feature pixels greater than two standard deviations over the background
Ratio_of_Means Unnormalized ratio of means defined by CH1/CH2
AREA Number of feature pixels
BKD_AREA Number of feature background pixels
CH1_Median-CH1_BKD Channel 1 median signal
CH2_Median-CH2_BKD Channel 2 median signal
CH1_Mean-CH1_BKD Channel 1 mean signal
CH2_Mean-CH2_BKD Channel 2 mean signal
PRE_VALUE Normalized ratio of means defined by CH1/CH2

Data table
ID_REF VALUE CH1_Median CH1_MEAN CH1_SD CH1_BKD_Median CH1_BKD_MEAN CH1_BKD_SD %>CH1_BKD_+2SD CH2_Median CH2_MEAN CH2_SD CH2_BKD_Median CH2_BKD_MEAN CH2_BKD_SD %>CH2_BKD_+2SD Ratio_of_Means AREA BKD_AREA CH1_Median-CH1_BKD CH2_Median-CH2_BKD CH1_Mean-CH1_BKD CH2_Mean-CH2_BKD PRE_VALUE
5269516 2.6137 15852 16085 2414 69 74 27 100 2790 2698 731 97 100 34 99 6.1580000000000004 120 759 15783 2693 16011 2598 6.1209062426670249
5269517 2.3507 13771 13833 2573 76 81 29 100 2804 2782 655 101 107 45 100 5.1310000000000002 120 865 13695 2703 13752 2675 5.1006901522606229
5269518 0.2621 326 324 66 61 65 21 100 308 319 94 101 105 38 91 1.206 120 730 265 207 259 214 1.1992266583982338
5269519 0.4680 690 684 160 62 68 27 99 565 553 191 106 110 36 98 1.391 120 768 628 459 616 443 1.3831996833317761
5269520 0.9033 1642 1671 244 66 76 66 100 947 981 224 128 136 53 100 1.8819999999999999 80 626 1576 819 1595 845 1.8703721399621025
5269521 -0.1197 248 248 74 73 79 32 94 311 310 98 121 124 40 86 .92600000000000005 120 744 175 190 169 186 .92040350489654632
5269522 -0.1572 825 819 114 63 67 25 100 965 966 202 128 135 48 100 .90200000000000002 80 628 762 837 752 831 .89676736715743688
5269523 -0.2108 638 628 128 63 67 24 100 757 753 192 103 106 36 99 .86899999999999999 120 768 575 654 561 647 .86404649028903469
5269524 -0.2991 354 353 86 93 99 41 98 425 430 103 112 116 38 100 .81799999999999995 120 822 261 313 254 314 .81273366092751642
5269525 0.0187 283 286 78 73 77 24 100 291 306 87 97 103 43 93 1.0189999999999999 80 636 210 194 209 203 1.013060393619146
5269526 -0.2664 838 810 171 74 79 29 99 1016 979 252 99 104 41 97 .83599999999999997 120 756 764 917 731 875 .83137538405928024
5269527 -0.3037 214 209 47 68 71 21 97 265 272 93 99 103 38 81 .81499999999999995 80 644 146 166 138 169 .81016789436789627
5269528 1.1781 417 412 117 66 69 23 99 238 241 82 89 95 34 85 2.2759999999999998 120 706 351 149 343 146 2.2627393533535618
5269529 1.4057 737 752 181 67 70 20 100 351 357 110 100 105 39 95 2.665 120 836 670 251 682 252 2.6494728129278791
5269530 0.5651 684 700 205 63 67 22 100 538 536 180 108 113 42 94 1.488 156 911 621 430 633 423 1.4794411103472616
5269531 -0.3513 585 570 145 59 64 25 98 754 754 196 106 108 36 100 .78900000000000003 120 735 526 648 506 646 .78387698500355851
5269532 2.5277 2485 2568 740 62 67 24 100 559 555 154 123 125 40 98 5.8010000000000002 120 734 2423 436 2501 430 5.7663279581768618
5269533 -0.0579 697 731 228 69 76 30 100 796 806 297 121 123 38 96 .96599999999999997 120 718 628 675 655 683 .96065940125669302
5269534 1.3616 553 550 113 64 67 22 100 340 330 94 142 156 72 65 2.585 120 752 489 198 483 174 2.5696882534579748
5269535 -0.2013 293 295 68 64 69 24 100 352 367 119 103 108 42 95 .875 120 706 229 249 226 259 .86978131212723619

Total number of rows: 16512

Table truncated, full table size 2035 Kbytes.




Supplementary data files not provided
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